Psaila-Wang-et al-Molecular Cell-2020-Figure2A-C

Figure2A-C

High-throughput single cell RNA-sequencing of 120,196 CD34+Lin- HSPCs from 21 donors reveals marked expansion of megakaryocyte progenitors (MkP) in myelofibrosis.

note: The objects was built based on SingCellaR beta version. The figures are reproduced using SingCellaR v1.2.0

load the library and object

library(SingCellaR)

## Warning: replacing previous import 'ComplexHeatmap::pheatmap' by
## 'pheatmap::pheatmap' when loading 'SingCellaR'

library(ggplot2)
load(file = "~/Downloads/Psaila_Wang_MC/All_merged_combat_v1.rdata")

2A: Dimensionality reduction using Uniform Manifold Approximation and Projection (UMAP) of an aggregate of all control (n=37,941) and myelofibrosis (n=82,255) cells identified 8 distinct cell clusters. Cells were partitioned using the Louvain community-detection clustering method and annotated according to expression of key marker genes for major hematopoietic cell types (see also Suppl. Table 4). Abbreviations: HSPC – hematopoietic stem/progenitor cells; Mye – myeloid progenitor; Ery – erythroid progenitor; Lymph – lymphoid progenitor; MkP – megakaryocyte progenitors.

2B: Expression of lineage signature gene sets were superimposed on the UMAP (grey = uncommitted or expression of >1 lineage gene set, See also Suppl. Table 5).Brown - MF, Blue - HD.

2C: Cells in UMAP plot coloured according to donor type (healthy donors – blue; myelofibrosis – red). The gmt file can be found in this github repository.